Methods and reagents for molecular cloning

Details Methods and reagents for molecular cloning Methods and reagents for molecular cloning

2005-07-12

2005-07-12

Fredman, Jeffrey (Department: 1637)

Chemistry: molecular biology and microbiology

Micro-organism, tissue cell culture or enzyme using process...

Preparing compound containing saccharide radical

C435S091500, C435S091410, C435S069100, C435S233000, C435S320100, C536S023100, C536S024200, C536S024300, C530S350000

Reexamination Certificate

active

06916632

ABSTRACT:
The present invention provides compositions, methods, and kits for covalently linking nucleic acid molecules. The methods include a strand invasion step, and the compositions and kits are useful for performing such methods. For example, a method of covalently linking double stranded (ds) nucleic acid molecules can include contacting a first ds nucleic acid molecule, which has a topoisomerase linked to a 3′ terminus of one end and has a single stranded 5′ overhang at the same end, with a second ds nucleic acid molecule having a blunt end, such that the 5′ overhang can hybridize to a complementary sequence of the blunt end of the second nucleic acid molecule, and the topoisomerase can covalently link the ds nucleic acid molecules. The methods are simpler and more efficient than previous methods for covalently linking nucleic acid sequences, and the compositions and kits facilitate practicing the methods, including methods of directionally linking two or more ds nucleic acid molecules.

REFERENCES:
patent: 4661450 (1987-04-01), Kempe
patent: 4800159 (1989-01-01), Mullis
patent: 5624826 (1997-04-01), Kato et al.
patent: 5766891 (1998-06-01), Shuman
patent: 5958681 (1999-09-01), Wetmur et al.
patent: 6013440 (2000-01-01), Lipshutz et al.
patent: 6140086 (2000-10-01), Fox et al.
patent: 6238884 (2001-05-01), Short et al.
patent: 6277632 (2001-08-01), Harney
patent: 6280977 (2001-08-01), Liang
patent: 6291213 (2001-09-01), Rothstein
patent: 6340595 (2002-01-01), Vogels et al.
patent: 6537776 (2003-03-01), Short
patent: 6548277 (2003-04-01), Shuman
patent: 2001/0044137 (2001-11-01), Heyman et al.
patent: 2002/0025561 (2002-02-01), Hodgson
patent: 2002/0028444 (2002-03-01), Harney et al.
patent: 2002/0068290 (2002-06-01), Yarovinsky
patent: 2002/0182731 (2002-12-01), Ji et al.
patent: 0 373 914 (1989-12-01), None
patent: 0 625 572 (1993-09-01), None
patent: 85/04898 (1985-11-01), None
patent: 94/29443 (1994-12-01), None
patent: 96/19497 (1996-06-01), None
patent: 96/34981 (1996-11-01), None
patent: 97/24455 (1997-07-01), None
patent: WO 97/48716 (1997-12-01), None
patent: 98/20122 (1998-05-01), None
patent: 98/55502 (1998-12-01), None
patent: 98/56943 (1998-12-01), None
patent: WO 00/12687 (2000-03-01), None
patent: 00/56878 (2000-09-01), None
patent: WO 01/62892 (2001-08-01), None
Liu, et al., “Mapping the 5′ and 3′ Ends ofTetrahymena thermophilamRNAs Using RNA Ligase Mediated Amplification of cDNA Ends (RLM-RACE),”Nucleic Acids Research21(21): 4954-4960. (1993) The Oxford University Press.
Lockard, et al., “Labeling of Eukaryotic Messager RNA 5′ Terminus with Phosphorus-32: Use of Tobacco Acid Pyrophosphatase for Removal of Cap Structures,”Gene Amplification and Analysis2:229-251. (1981) Elsevier Science.
Wexler, et al., “A Procedure to Amplify cDNA from dsRNA Templates Using the Polymerase Chain Reaction,”Methods in Molecular and Cellular Biology2:273-279 (1991).
Carninci, et al., “High-Efficiency Full-Length cDNA Cloning by Biotinylated CAP Trapper,”Genomics,37(3):327-36 (1996) Academic Press, Inc.
Carninci et al., “High Efficiency Selection of full-length cDNA by Improved Biotinylated Cap Trapper,”DNA Research,4:61-66 (1997). Universal Academy Press.
Cheng and Shuman, “DNA strand transfer catalyzed by vaccinia topoisomerase: ligation of DNAs containing a 3′ mononucleotide overhang,”Nucleic Acids Res.,28(9):1893-8. (2000). Oxford University Press.
Cheng and Shuman, “Recombinogenic flap ligation pathway for intrinsic repair of topoisomerase IB-induced double-strand breaks,”Mol. Cell. Biol.20(21):8059-8068 (2000) American Society for Microbiology.
Cheng and Shuman, “Site-specific DNA transesterification by vaccinia topoisomerase: Role of specific phosphates and nucleosides,”Biochemistry38(50):16599-612 (1999) American Chemical Society.
Cheng and Shuman, “A catalytic domain of eukaryotic DNA topoisomerase I,”J. Biol. Chem.273(19):11589-95 (1988). The American Society for Biochemistry and Molecular Biology, Inc.
Cheng, et al., “Conservation of structure and mechanism between eukaryotic topoisomerase I and site-specific recombinases,”Cell.92(6):841-50 (1998) Cell Press.
Cheng, et al., “Mutational analysis of 39 residues of vaccinia DNA topoisomerase identifies Lys-220, Arg-223, and Asn-228 as important for covalent catalysis,”J. Biol. Chem.272(13):8263-9 (1997) The American society for Biochemistry and Molecular Biology, Inc.
DiGate and Marians, “Molecular Cloning and DNA Sequence Analysis ofEscherichia colitopB, the Gene Encoding Topoisomerase III,”J. Biol. Chem.264(30):17924-17930 (1989). The American society for Biochemistry and Molecular Biology, Inc.
Edery, et al., “An Efficient Strategy to Isolate Full-Length cDNAs Based on an mRNA Cap Retention Procedure (CAPture),”Mol. Cell. Biol.,15(6):3363-3371 (1995). American Society for Microbiology.
Ericsson, et al., “Characterization of ts 16, a temperature-sensitive mutant of vaccinia virus,”J. Virol..69(11):7072-86 (1995) American Society for Microbiology.
Gross and Shuman, “Vaccinia virions lacking the RNA helicase nucleoside triphosphate phosphohydrolase II are defective in early transcription,”J. Virol.70(12):8549-5 (1996) American Society for Microbiology.
Haghighat and Sonenberg. “eIF4G Dramatically Enhances the Binding of eIF4E to the mRNA 5′-Cap Structure,”J. Biol. Chem.,272(35):21677-21680 (1997). The American society for Biochemistry and Molecular Biology, Inc.
Haghighat et al., “The eIF4G-eIF4E Complex is the Target for Direct Cleavage by the Rhinovirus 2A Proteinase,”J. Virol.70:8444-8450 (1996). American Society for Microbiology.
Henningfeld and Hecht, “A model for topoisomerase I-mediated insertions and deletions with duplex DNA substrates containing branches, nicks, and gaps,”Biochemistry34(18):6120-9. (1995) American Chemical Society.
Invitrogen Corporation.Invitrogen Catalog,Carlsbad, California, pp. 18, 29, 43, 44, 49-52 (1998).
Janknecht, et al., “Rapid and efficient purification of native histidine-tagged protein expressed by recombinant vaccinia virus,”Proc. Natl. Acad. Sci., U S A88:8972-8976(1991) National Academic of Sciences.
Kane and Shuman, “Vaccinia virus morphogenesis is blocked by a temperature-sensitive mutation in the 17 gene that encodes a virion component,”J. Virol.67(5)::2689-98 (1993) American Society for Microbiology.
Kato, et al., “Construction of a Human Full-Length cDNA Bank,”Gene.150: 243-250 (1994) Elsevier Science.
Klemm, et al., “Peptide inhibitors of DNA cleavage by tyrosine recombinases and topoisomerases,”J. Mol. Biol.299(5):1203-16. (2000) Academic Press, Inc.
Klemperer, et al., “Identification and characterization of the orf virus type I topoisomerase,”Virology206:203-215 (1995) Academic Press, Inc.
Krogh and Shuman, “Vaccinia topoisomerase mutants illuminate conformational changes during closure of the protein clamp and assembly of a functional active site,”J. Biol. Chem.Jul. 5, 2001 [Manuscript] The American Society for Biochemistry and Molecular Biology, Inc.
Krogh and Shuman, “Catalytic mechanism of DNA topoisomerase IB,”Mol. Cell.,5(6):1035-41 (2000) Cell Press.
Krogh and Shuman, “DNA strand transfer catalyzed by vaccinia topoisomerase: peroxidolysis and hydroxylaminolysis of the covalent protein-DNA intermediate,”Biochemistry39(21):6422-32. (2000) American Chemical Society.
Krogh, et al., “Effect of 2′-5′ phosphodiesters on DNA transesterification by vaccinia topoisomerase,”J. Biol. Chem.276(24):20907-20912. (2001) The American Society for Biochemistry and Molecular Biology, Inc.
Krogh, et al.,Melanoplus sanguinipesentomopoxvirus DNA topoisomerase: site-specific DNA transesterification and effects of 5′-bridging phosphorothiolates,Virolo

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